BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082936.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,845,179 number of mapped reads = 1,699,817 (92.12%) number of supplementary alignments = 18,221 (0.99%) number of secondary alignments = 0 number of mapped bases = 115,088,605 bp number of sequenced bases = 115,043,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,571 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3955 >>>>>>> ACTG content number of A's = 32,152,471 bp (27.95%) number of C's = 21,138,680 bp (18.37%) number of T's = 36,756,489 bp (31.95%) number of G's = 24,990,656 bp (21.72%) number of N's = 5,246 bp (0%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 823,895 number of insertions = 9,669 mapped reads with insertion percentage = 0.56% number of deletions = 27,620 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0372X std coverageData = 0.3071X There is a 3.14% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9286657 0.037258310381501514 0.37764029742690153 chr2 243199373 12311658 0.05062372426428912 0.4358316085831837 chr3 198022430 8942157 0.045157293544978716 0.24223853229645084 chr4 191154276 6056846 0.03168564222963027 0.2105065813058638 chr5 180915260 6228470 0.034427554646302365 0.21273857247473818 chr6 171115067 8252097 0.048225425993609315 0.3311118692627103 chr7 159138663 6378018 0.04007836863628796 0.29259786395429027 chr8 146364022 9357259 0.06393141478443384 0.4253650410069787 chr9 141213431 2852638 0.020200897179532447 0.2859336792216426 chr10 135534747 4247244 0.0313369382686788 0.23828781452492115 chr11 135006516 4048525 0.029987626671293406 0.26489094099167504 chr12 133851895 3662666 0.027363572252749952 0.19471173650605825 chr13 115169878 2776440 0.02410734515148136 0.1782372710062207 chr14 107349540 2782282 0.02591796853530998 0.20736551360788696 chr15 102531392 2043790 0.019933309790624906 0.16833537350130923 chr16 90354753 5750211 0.06364038203944844 0.3113643404321368 chr17 81195210 2464861 0.030357221811483707 0.21891180228405785 chr18 78077248 4442483 0.056898560256631994 0.7334738956066755 chr19 59128983 1183045 0.02000786991381198 0.29049281182535386 chr20 63025520 2649383 0.04203667022501361 0.24613141936805352 chr21 48129895 3064592 0.06367335727617938 0.294193530926229 chr22 51304566 1861265 0.03627873979091841 0.21581128829091337 chrMT 16571 8949 0.5400398286162573 0.8460903797833681 chrX 155270560 4259015 0.027429636371505327 0.21654886485178182 chrY 59373566 178054 0.0029988766381321952 0.0667773634933281